When opening BAM files in Golden helix genome browse 3.0.0 my coverage track is no longer grey (only colored if there is a variant present). Now, the bases are colored like in the reference sequence track (green, yellow, red and blue) and my variants are shown in the coverage track and no longer the pile-up track as it used to. Is this a new setting, and can I set it back?! The software is useless to me now, with these new settings.
Hi Signe,
The coverage track is gray when the correct reference sequence has been detected and so we can evaluate the match of the BAM letters to the reference (gray meaning matching bases, colored when mismatching).
First thing to check is that you have the appropriate reference sequences downloaded. You may have deleted the local reference sequence or you may be looking at BAMs with new assembly builds.
Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.
Asked: 2020-09-08 06:58:02 -0600
Seen: 2,107 times
Last updated: Sep 08 '20
